X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=getotulabelscommand.cpp;fp=getotulabelscommand.cpp;h=40ad69f771c0b7b58602666c22d0c4587486ebdf;hb=e0b6040c7b6ad4ecdad4aa90b4326c0528379178;hp=0000000000000000000000000000000000000000;hpb=e7ae6e6b27c45b5691c19f423ec56faae8e2f255;p=mothur.git diff --git a/getotulabelscommand.cpp b/getotulabelscommand.cpp new file mode 100644 index 0000000..40ad69f --- /dev/null +++ b/getotulabelscommand.cpp @@ -0,0 +1,381 @@ +// +// getotulabelscommand.cpp +// Mothur +// +// Created by Sarah Westcott on 5/21/12. +// Copyright (c) 2012 Schloss Lab. All rights reserved. +// + +#include "getotulabelscommand.h" + +//********************************************************************************************************************** +vector GetOtuLabelsCommand::setParameters(){ + try { + CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos); + CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pconstaxonomy); + CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(potucorr); + CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pcorraxes); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetOtuLabelsCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string GetOtuLabelsCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The get.otulabels command can be used to select specific otus with the output from classify.otu, otu.association, or corr.axes.\n"; + helpString += "The get.otulabels parameters are: constaxonomy, otucorr, corraxes, and accnos.\n"; + helpString += "The constaxonomy parameter is input the results of the classify.otu command.\n"; + helpString += "The otucorr parameter is input the results of the otu.association command.\n"; + helpString += "The corraxes parameter is input the results of the corr.axes command.\n"; + helpString += "The get.otulabels commmand should be in the following format: \n"; + helpString += "get.otulabels(accnos=yourListOfOTULabels, corraxes=yourCorrAxesFile)\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "GetOtuLabelsCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +GetOtuLabelsCommand::GetOtuLabelsCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["contaxonomy"] = tempOutNames; + outputTypes["otu.corr"] = tempOutNames; + outputTypes["corr.axes"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "GetOtuLabelsCommand", "GetOtuLabelsCommand"); + exit(1); + } +} +//********************************************************************************************************************** +GetOtuLabelsCommand::GetOtuLabelsCommand(string option) { + try { + abort = false; calledHelp = false; + + //allow user to run help + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} + + else { + //valid paramters for this command + vector myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + map::iterator it; + //check to make sure all parameters are valid for command + for (it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + + //edit file types below to include only the types you added as parameters + + string path; + it = parameters.find("constaxonomy"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["constaxonomy"] = inputDir + it->second; } + } + + it = parameters.find("accnos"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["accnos"] = inputDir + it->second; } + } + + it = parameters.find("corraxes"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["corraxes"] = inputDir + it->second; } + } + + it = parameters.find("otucorr"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["otucorr"] = inputDir + it->second; } + } + } + + vector tempOutNames; + outputTypes["contaxonomy"] = tempOutNames; + outputTypes["otu.corr"] = tempOutNames; + outputTypes["corr.axes"] = tempOutNames; + + //check for parameters + accnosfile = validParameter.validFile(parameters, "accnos", true); + if (accnosfile == "not open") { abort = true; } + else if (accnosfile == "not found") { + accnosfile = m->getAccnosFile(); + if (accnosfile != "") { m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine(); + abort = true; + } + }else { m->setAccnosFile(accnosfile); } + + constaxonomyfile = validParameter.validFile(parameters, "constaxonomy", true); + if (constaxonomyfile == "not open") { constaxonomyfile = ""; abort = true; } + else if (constaxonomyfile == "not found") { constaxonomyfile = ""; } + + corraxesfile = validParameter.validFile(parameters, "corraxes", true); + if (corraxesfile == "not open") { corraxesfile = ""; abort = true; } + else if (corraxesfile == "not found") { corraxesfile = ""; } + + otucorrfile = validParameter.validFile(parameters, "otucorr", true); + if (otucorrfile == "not open") { otucorrfile = ""; abort = true; } + else if (otucorrfile == "not found") { otucorrfile = ""; } + + + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; } + + if ((constaxonomyfile == "") && (corraxesfile == "") && (otucorrfile == "")) { m->mothurOut("You must provide one of the following: constaxonomy, corraxes or otucorr."); m->mothurOutEndLine(); abort = true; } + } + + } + catch(exception& e) { + m->errorOut(e, "GetOtuLabelsCommand", "GetOtuLabelsCommand"); + exit(1); + } +} +//********************************************************************************************************************** + +int GetOtuLabelsCommand::execute(){ + try { + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + //get labels you want to keep + readAccnos(); + + if (m->control_pressed) { return 0; } + + //read through the correct file and output lines you want to keep + if (constaxonomyfile != "") { readClassifyOtu(); } + if (corraxesfile != "") { readCorrAxes(); } + if (otucorrfile != "") { readOtuAssociation(); } + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + //output files created by command + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); + + return 0; + } + catch(exception& e) { + m->errorOut(e, "GetOtuLabelsCommand", "execute"); + exit(1); + } +} +//********************************************************************************************************************** +int GetOtuLabelsCommand::readClassifyOtu(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(constaxonomyfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile)) + "pick.taxonomy"; + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(constaxonomyfile, in); + + bool wroteSomething = false; + int selectedCount = 0; + + //read headers + string headers = m->getline(in); + out << headers << endl; + + while (!in.eof()) { + + if (m->control_pressed) { break; } + + string otu = ""; string tax = "unknown"; + int size = 0; + + in >> otu >> size >> tax; m->gobble(in); + + if (labels.count(otu) != 0) { + wroteSomething = true; + selectedCount++; + + out << otu << '\t' << size << '\t' << tax << endl; + } + } + in.close(); + out.close(); + + if (wroteSomething == false) { m->mothurOut("Your file does not contain any labels from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); outputTypes["constaxonomy"].push_back(outputFileName); + + m->mothurOut("Selected " + toString(selectedCount) + " otus from your constaxonomy file."); m->mothurOutEndLine(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "GetOtuLabelsCommand", "readClassifyOtu"); + exit(1); + } +} +//********************************************************************************************************************** +int GetOtuLabelsCommand::readOtuAssociation(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(otucorrfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile)) + "pick.corr"; + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(otucorrfile, in); + + bool wroteSomething = false; + int selectedCount = 0; + + //read headers + string headers = m->getline(in); + out << headers << endl; + + while (!in.eof()) { + + if (m->control_pressed) { break; } + + string otu1 = ""; + string otu2 = ""; + in >> otu1 >> otu2; + string line = m->getline(in); m->gobble(in); + + if ((labels.count(otu1) != 0) && (labels.count(otu2) != 0)){ + wroteSomething = true; + selectedCount++; + + out << otu1 << '\t' << otu2 << '\t' << line << endl; + } + } + in.close(); + out.close(); + + if (wroteSomething == false) { m->mothurOut("Your file does not contain any labels from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); outputTypes["otu.corr"].push_back(outputFileName); + + m->mothurOut("Selected " + toString(selectedCount) + " lines from your otu.corr file."); m->mothurOutEndLine(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "GetOtuLabelsCommand", "readOtuAssociation"); + exit(1); + } +} +//********************************************************************************************************************** +int GetOtuLabelsCommand::readCorrAxes(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(corraxesfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile)) + "pick.axes"; + ofstream out; + m->openOutputFile(outputFileName, out); + + + ifstream in; + m->openInputFile(corraxesfile, in); + + bool wroteSomething = false; + int selectedCount = 0; + + //read headers + string headers = m->getline(in); + out << headers << endl; + + while (!in.eof()) { + + if (m->control_pressed) { break; } + + string otu = ""; + in >> otu; + string line = m->getline(in); m->gobble(in); + + if (labels.count(otu) != 0) { + wroteSomething = true; + selectedCount++; + + out << otu << '\t' << line << endl; + } + } + in.close(); + out.close(); + + if (wroteSomething == false) { m->mothurOut("Your file does not contain any labels from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); outputTypes["corr.axes"].push_back(outputFileName); + + m->mothurOut("Selected " + toString(selectedCount) + " lines from your corr.axes file."); m->mothurOutEndLine(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "GetOtuLabelsCommand", "readCorrAxes"); + exit(1); + } +} + +//********************************************************************************************************************** +int GetOtuLabelsCommand::readAccnos(){ + try { + + ifstream in; + m->openInputFile(accnosfile, in); + string name; + + while(!in.eof()){ + in >> name; + + labels.insert(name); + + m->gobble(in); + } + in.close(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "GetOtuLabelsCommand", "readAccnos"); + exit(1); + } +} +//**********************************************************************************************************************